Summer Research Institute | 2013 Research

Study of the refined Gaussian Network Model (GNM) for HIV-1 protease

Jun-Koo Park, assistant professor of mathematics, and two students, Jacob Liddle and Nicholas Fuller, will continue their study of the refined Gaussian Network Model (GNM) for HIV-1 protease. The HIV-1 protease plays an essential role in the life cycle of HIV. Accurate predictions on its structural fluctuations may provide great insights into how the dynamics of the structure relate to their functions. The goal of this study is to refine the non-homogeneous GNM and apply it to the recently modeled structure, HIV-1 protease.

Community detection in social networks

Wei Hu, professor of math and computer science, will be researching with two computer science students, Brian Dickinson and Benjamin Valyou, and Dr. Xumin Liu from RIT, on community detection in social networks. Through learning of the community structures in social networks, we attain the knowledge of the formation, split, merge, and evolution of these communities. However, identification of communities in a real network is a challenge since the number and the sizes of communities are typically unknown. Additionally large networks of millions of nodes can bring great computational difficulty. The goal of this study is to explore an integrative approach to community detection.

Biodegradable Glycopolymers

John Rowley, assistant professor of chemistry, and students Ethan Kent and Jason Orlando will be developing methods for the synthesis of biodegradable materials. Glycopolymers are a particularly interesting class of materials as they contain chemical functionalities that mimic signaling receptors on the surface of cells. Biodegradable glycopolymers that can degrade or be absorbed by the body have potential applications in drug-delivery, tissue engineering, and biomedical research.

Salamanders within the family Plethodontidae are excellent models for investigating how terrestrial prey use chemical cues to evaluate predation risk. Members of this family are equipped with well-developed chemosensory organs and rely on chemical cue detection for functions such as foraging, territory maintenance, and mate recognition. Furthermore, some species respond to chemical stimuli from predators and even injured salamanders. In this study, Aaron Sullivan, associate professor of biology and two students including Julia Dyer will hope to address the degree to which behavioral responses by prey are fine-tuned by the internal state of the salamander (e.g., experience, hunger levels). The first line of research will evaluate how recently attacked individuals will respond to chemical cues from predators. To accomplish this we will induce tail autotomy in a subset of our salamander population to simulate predation. (Tail autotomy is commonly employed by a number of salamanders upon contact with predators as a means of escape). It is possible that salamanders with recent experience related to predation may respond more strongly to chemical stimuli from predators or that injured salamanders may be more likely to forage in the presence of predator cues because their primary energy storage organ (i.e. their tail) has been lost. The second line of research will attempt to understand how ‘hunger’ levels influence antipredator decision-making by maintaining animals on different food regimes (e.g., no food vs ad libitum feeding). Satiated individuals may be more inclined to engage in risk-averse behavior whereas ‘hungry’ salamanders may be more risk-prone and willing to forage when predation risk is relatively high.

Macroarray detection of RNA viral plant pathogens in Vitis vinifera and related grapevine species of western New York

Jamie Potter, Assistant Professor of Biology, will be working with 2 students in collaboration with Dr. Keith Perry, Associate Professor at Cornell University Department of Plant Pathology and Plant-Microbe Biology, on the detection of plant RNA viruses in grapevine. We will be focusing on Grapevine leaf roll-associated viruses, GLRaV, in Vitis vinifera and related Vitis species through collection and analysis of plant samples from western New York vineyards and adjacent wild cultivars using newly developed molecular macroarray diagnostic techniques. This work is supported by the Houghton College Moreland Research Fund.

Thin metal films

Brandon Hoffman, assistant professor of physics, and two students (Ethan Ocock and Emily Morrow) will be collaborating with Shefford Baker at the Center for Materials Research (CCMR) at Cornell University. Today’s technology requires the use of metal films with thicknesses of only a few hundred nanometers or less. Not much is known about the properties of materials this small and the present models do not accurately describe the films. Therefore, thin silver films will be produced in a high vacuum deposition chamber and studied with x-ray diffraction (XRD) and electron backscatter diffraction (EBSD) in order to characterize the microstructures and transformations of the films. The goal of these experiments will be to improve the general model that describes similar thin metal films.

Inertial confinement fusion

Mark Yuly, professor of physics, and two students, Garrett Hartshaw and Ian Love, will be working with scientists from SUNY-Geneseo and Ohio University on research related to inertial confinement fusion (ICF). In ICF a large amount of energy is deposited, usually with high-powered lasers, to a small pellet of nuclear fuel in order to initiate a fusion reaction. In order to characterize the fusion reaction, a system has been developed using 12C activation. Samples of purified graphite are placed at several locations around the ICF target chamber, where they are exposed to the flux of neutrons produced in the fusion reaction. By far, the biggest remaining obstacle to the implementation of this diagnostic technique is that it depends on accurate knowledge of the 12C(n,2n) cross section, which has not been well-measured. Last summer we carried out a feasibility study for a measurement of this cross section; this summer we will measure this cross section up to the highest energy possible using the tandem accelerator at the John E. Edwards Accelerator Laboratory at Ohio University.

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